gusdev-gusdev

[Gusdev-gusdev] ReviewStatus issues

[Steve F. <sfi...@pc...>]

Folks-

I am discovering other controlled vocab issues.

First, ReviewStatus.

On the wiki, there is a set of values for this:
  annotated
  not reviewed
  unknown

At CBIL, we have:
reviewed, correct
unreviewed
reviewed, incorrect
updated
needs re-review

What's worse, many tables required a non-null ReviewStatus, and many 
plugins use hard-coded review_status_ids in the code.

Often, the logic of a plugin is "update this row with the newly-computed 
data, unless the row has been reviewed (review_status_id == 1), in which 
case, assume it is correct, and leave it alone."  

My feeling is that ReviewStatus should be optional.

So, i think that it should always be nullable.

I also think that different sites will want to define this differently.

So, I would say that:
  1. plugins that test review status to decide whether to update the 
data or not should take on their command line a list of review status 
terms that indicate "don't update."    The plugin should query the db to 
find the review_status_ids for those (failing if not found).  If none 
are supplied to the plugin, then the plugin should not bother checking 
review status.

 2. plugins that write review status info should take a mapping from the 
values found in the input to review status  terms.  They should check 
that the review status terms are in the db, failing if not.  then, they 
can map the input to the proper review status id, and write the data to 
the db.

The upshot is that i don't think the GUS install should provide values 
for ReviewStatus.   It should be optional and site specific.

steve

Re: [Gusdev-gusdev] ReviewStatus issues

[<ju...@cs...>]

Steve Fischer <sfi...@pc...> writes:
>
> I am discovering other controlled vocab issues.
>
> First, ReviewStatus.

Speaking of ReviewStatus, I wrote concerning this
field and the DoTS.NAFeature table a few days ago.

Will this field be present in the NAFeature table
in version 3.5?  Is it there now in version 3.2?


> The upshot is that i don't think the GUS install should provide values
> for ReviewStatus.   It should be optional and site specific.

I completely agree. See below.

Thanks, Josef


My previous mail:
=>
=>  From: Josef Jurek <ju...@cs...>
=>  To: gus...@li...
=>  Message-Id: <200...@ga...>
=>  Subject: [Gusdev-gusdev] Another necessary field
=>  Date: Tue,  1 Feb 2005 17:35:11 -0600 (CST)
=>
=>
=>  According to the schema browser, DoTS.NAFeature has
=>  the field review_status_id which of course
=>  points to a row in the table SRes.ReviewStatus.
=>  However, in my installation of GUS, schema version 3.0,
=>  DoTS.NAFeature lacks this field.
=>
=>  Such a thing would be very useful to have to distinguish
=>  between the annotation of the same sequence by
=>  different organizations.
=>
=>  In fact, I could use this field right now.  Does
=>  schema version 3.2 have this field?  If so,
=>  can someone suggest a patch/rebuild method
=>  so that I could at least upgrade the NAFeature
=>  table in my installation?
=>
=>  Thanks, Josef
=>




Josef Jurek, Ph.D.

Daphne Preuss Laboratory
Molecular Genetics and Cell Biology
The University of Chicago
ju...@cs...

voice: (773) 834-3985
fax:   (773) 702-6648

Re: [Gusdev-gusdev] ReviewStatus issues

[Steve F. <sfi...@pc...>]

josef-

a few things.

yes, that attribute will be in 3.5.

patching it is kind of a pain.

i'm wondering if your use case might be better satisfied by using 
prediction algorithm or the external_database_release_id to track who 
made the feature.  (conceptually review status has to do with what the 
curators have done to the feature).

if you still want to patch it, let me know and we'll describe how.

steve

Josef Jurek wrote:

>Steve Fischer <sfi...@pc...> writes:
>  
>
>>I am discovering other controlled vocab issues.
>>
>>First, ReviewStatus.
>>    
>>
>
>Speaking of ReviewStatus, I wrote concerning this
>field and the DoTS.NAFeature table a few days ago.
>
>Will this field be present in the NAFeature table
>in version 3.5?  Is it there now in version 3.2?
>
>
>  
>
>>The upshot is that i don't think the GUS install should provide values
>>for ReviewStatus.   It should be optional and site specific.
>>    
>>
>
>I completely agree. See below.
>
>Thanks, Josef
>
>
>My previous mail:
>=>
>=>  From: Josef Jurek <ju...@cs...>
>=>  To: gus...@li...
>=>  Message-Id: <200...@ga...>
>=>  Subject: [Gusdev-gusdev] Another necessary field
>=>  Date: Tue,  1 Feb 2005 17:35:11 -0600 (CST)
>=>
>=>
>=>  According to the schema browser, DoTS.NAFeature has
>=>  the field review_status_id which of course
>=>  points to a row in the table SRes.ReviewStatus.
>=>  However, in my installation of GUS, schema version 3.0,
>=>  DoTS.NAFeature lacks this field.
>=>
>=>  Such a thing would be very useful to have to distinguish
>=>  between the annotation of the same sequence by
>=>  different organizations.
>=>
>=>  In fact, I could use this field right now.  Does
>=>  schema version 3.2 have this field?  If so,
>=>  can someone suggest a patch/rebuild method
>=>  so that I could at least upgrade the NAFeature
>=>  table in my installation?
>=>
>=>  Thanks, Josef
>=>
>
>
>
>
>Josef Jurek, Ph.D.
>
>Daphne Preuss Laboratory
>Molecular Genetics and Cell Biology
>The University of Chicago
>ju...@cs...
>
>voice: (773) 834-3985
>fax:   (773) 702-6648
>
>  
>

Re: [Gusdev-gusdev] ReviewStatus issues

[<ju...@cs...>]

Steve Fischer <sfi...@pc...> writes:
=>
=> [...]
=>
=> yes, that attribute will be in 3.5.
=> patching it is kind of a pain.
=>
=> i'm wondering if your use case might be better satisfied by using
=> prediction algorithm or the external_database_release_id to track who
=> made the feature.

prediction_algorithm_id, like review_status_id, does not exist
in schema version 3.0.

As for external_database_release_id  I suppose that could be
used.  So far, we have only used the External_Database/External_Database_Release
tables to identify collections of sequences.  Would this
not be against the conception of the schema to use these tables
to identify collections of features?

=> (conceptually review status has to do with what the
=> curators have done to the feature).

If one considers that the first step of the curator is to
identify a feature, then perhaps there is no conflict
between your conceptual use of SRes.ReviewStatus
and the use I have suggested?  One of the suggested
values for SRes.ReviewStatus.name, "annotated",
seems to cover this.

=> if you still want to patch it, let me know and we'll describe how.

If you could, that would be great.  There is probably no need to
send this to the list, unless others mention that they are
interested.

Thanks again!

Josef

=>
=> >My previous mail:
=> >=>
=> >=>  From: Josef Jurek <ju...@cs...>
=> >=>  To: gus...@li...
=> >=>  Message-Id: <200...@ga...>
=> >=>  Subject: [Gusdev-gusdev] Another necessary field
=> >=>  Date: Tue,  1 Feb 2005 17:35:11 -0600 (CST)
=> >=>
=> >=>
=> >=>  According to the schema browser, DoTS.NAFeature has
=> >=>  the field review_status_id which of course
=> >=>  points to a row in the table SRes.ReviewStatus.
=> >=>  However, in my installation of GUS, schema version 3.0,
=> >=>  DoTS.NAFeature lacks this field.
=> >=>
=> >=>  Such a thing would be very useful to have to distinguish
=> >=>  between the annotation of the same sequence by
=> >=>  different organizations.
=> >=>
=> >=>  In fact, I could use this field right now.  Does
=> >=>  schema version 3.2 have this field?  If so,
=> >=>  can someone suggest a patch/rebuild method
=> >=>  so that I could at least upgrade the NAFeature
=> >=>  table in my installation?
=> >=>
=> >=>  Thanks, Josef
=> >=>
=> >
=> >
=> >





Daphne Preuss Laboratory
Molecular Genetics and Cell Biology
The University of Chicago
ju...@cs...

voice: (773) 834-3985
fax:   (773) 702-6648